3-47381196-A-G
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_015466.4(PTPN23):c.84+16A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000051 in 1,570,112 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000042 ( 0 hom. )
Consequence
PTPN23
NM_015466.4 intron
NM_015466.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.89
Genes affected
PTPN23 (HGNC:14406): (protein tyrosine phosphatase non-receptor type 23) This gene encodes a member of the non-receptor type protein-tyrosine phosphatase family. The encoded protein may be involved in the regulation of small nuclear ribonucleo protein assembly and pre-mRNA splicing by modifying the survival motor neuron (SMN) complex. The encoded protein additionally plays a role in ciliogenesis and is part of endosomal sorting complex required for transport (ESCRT) pathways. This gene may serve a tumor suppressor function. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 3-47381196-A-G is Benign according to our data. Variant chr3-47381196-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1949725.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPN23 | NM_015466.4 | c.84+16A>G | intron_variant | ENST00000265562.5 | NP_056281.1 | |||
PTPN23 | NM_001304482.2 | c.-167+16A>G | intron_variant | NP_001291411.1 | ||||
PTPN23 | XM_005265031.3 | c.84+16A>G | intron_variant | XP_005265088.2 | ||||
PTPN23-DT | NR_185912.1 | n.297T>C | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPN23 | ENST00000265562.5 | c.84+16A>G | intron_variant | 1 | NM_015466.4 | ENSP00000265562.4 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152072Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000562 AC: 1AN: 177902Hom.: 0 AF XY: 0.0000105 AC XY: 1AN XY: 94938
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GnomAD4 exome AF: 0.00000423 AC: 6AN: 1418040Hom.: 0 Cov.: 31 AF XY: 0.00000570 AC XY: 4AN XY: 701544
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 152072Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74276
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 10, 2023 | - - |
Computational scores
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Benign
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Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at